Figure 2.
Genomic, phylogenetic, and molecular clock analyses of the B.1.427/B.1.429 variant in California
(A) A multiple sequence alignment of 6 representative B.1.427/B.1.429 genomes, 3 from the B.1.427 lineage, and 3 from the B.1.429 lineage, using the prototypical Wuhan Hu-1 genome as a reference. Defining single nucleotide polymorphisms (SNPs) in the B.1.427 and B.1.429 lineages are compared to each other and to other SARS-CoV-2 viruses in Nextstrain clade 20C. The SNPs are color coded as follows: red SNPs are shared between the B.1.427 and B.1.429 lineages, blue SNPs are specific to B.1.427, purple SNPs are specific to B.1.429, brown SNPs are shared with other clade 20C viruses, and gray SNPs are specific to individual viruses.
(B) Root-to-tip divergence plot of number of accumulated mutations by month based on 1,153 genomes subsampled from a complete dataset consisting of the 2,172 genomes recovered in the current study and 347 representative global genomes. The gray highlighted region encompasses the period of sampling for nearly all genomes sequenced in the current study (September 1, 2020 to January 31, 2021), with the exception of the first 2 sequenced B.1.429 genomes from Los Angeles that were reported on July 20, 2020. The orange-red bullseye denotes the first reported genomic sequence of the B.1.429 variant from Los Angeles County from a sample collected July 13, 2020.
(C) Maximum likelihood circular phylogenetic tree of the 1,153 subsampled genomes, denoting the major viral clades. The red asterisk denotes a UK B.1.1.7 variant genome.
(D) Time scaled maximum clade credibility (MCC) tree, showing the median divergence dates and associated 95% highest posterior density (HPD) distributions, or confidence intervals, for the B.1.427/B.1.429 variant (D1), B.1.429 lineage (D2), and B.1.427 lineage (D3), as estimated from TMRCA (time to most recent common ancestor) calculations. The B.1.427 lineage is colored in blue and the B.1.429 lineage in red. The orange-red bullseye denotes the first reported genomic sequence of the B.1.429 variant from Los Angeles County from a sample collected July 13, 2020.